An investigation was conducted to characterize flow, circulation, and transport in the Neuse River estuary, North Carolina. The study included a detailed field-measurement program and the calibration, validation, and application of a physically realistic numerical model of hydro- dynamics and transport through a 40-kilometer reach of the estuary. Water level, salinity, water temperature, wind speed and direction, current velocity, and bathymetric data were collected during March 1988 through September 1992. Additional data from pre-existing continuous-record streamflow gaging stations and meteorological stations also were used. A two-dimensional, vertically averaged hydrodynamic and solute transport model was applied to the study reach. The model domain was discretized into 200- by 200-meter computational cells. Model calibration was achieved through adjustment of model parameters for the period June 1-24, 1991. Additional simulations for periods in 1989 and 1991 were run to validate the model. The model was calibrated and validated for water levels ranging from -0.104 to 0.908 meters, salinities ranging from 2.8 to 22.0 parts per thousand, and wind speed from calm to 9 meters per second. The model was tested for stratified and unstratified conditions. Simulated and observed level, salinity, and velocity data were used to evaluate the model. The calibrated model was applied to simulate flows, circulation, and salinity distributions for four simulation periods in 1989 and 1991. Comparisons of simulated results for a period in June 1991 were made between the Neuse and Pamlico models to characterize differences between the two systems.